The BBC's Catherine Byaruhanga in Kampala says there has been criticism from some journalists who say the Nation Media Group has chosen to protect their business interests over their editorial policies.

The company said it lost thousands of dollars each day its newspapers and radio stations were closed.

The Daily Monitor's Managing Director, Alex Asiimwe, told the BBC the paper had not caved in to government pressure, but rather "reason had prevailed".

"It is not good thinking for people to say if they have opened us, then we have backed down," he told the BBC's Focus on Africa programme.

When asked if the paper "regretted" the story, he said it would prompt "self-reflection".

"When we produced that story we thought we had subjected it to the best [editorial policy guidelines] that we can."

Earlier this week, police tear-gassed and beat journalists with batons as they protested outside the offices of the Daily Monitor.

The authorities said they wanted evidence of how the Daily Monitor got hold of the confidential letter, purportedly written by Gen David Sejusa, who is out of the country.

In the government statement, it said the raid on 20 May 2013 was ordered because "it was established that the director general, Internal Security Organisation, to whom the letter was addressed, as well as the officers to whom the letter was copied never received it. Evidently, it was only the Daily Monitor in possession of the letter."

President Museveni and the management of Nation Media Group, which owns the Monitor, met on Sunday 26 May, it said.

They had agreed to "only publish or air stories which are properly sourced, verified and factual", amongst other undertakings, the statement from the Minister of Internal Affairs, Hilary Onek, said.

They also "undertook to be sensitive to and not publish or air stories that can generate tensions, ethnic hatred, cause insecurity or disturb law and order", it said.

Thanks to these agreements, the minister had ordered that the police remove the cordon at the Daily Monitor's office to allow "normal business as police continue with the search".

The government commended the Red Pepper publication for its co-operation during the crisis.